This study aimed to investigate whether suboptimal incubation (SI) temperature in weeks 1 and 3 of layer embryo incubation affects their development and post-hatch adaptive capacity during infectious challenges, by using Eimeria as a model infection under normal and immediately after more challenging environmental conditions of 72 h heat exposure. Eggs (n = 160 per treatment) were incubated at optimal (OI = 37.8°C continuously) or suboptimal eggshell temperature (36.7°C, 37.8°C and 38.9°C in weeks 1, 2 and 3, respectively). At day 33 of age, half the chickens of each incubation treatment were exposed to 72 h heat (35°C), whereas the other half remained under control conditions (21°C). At day 36 of age, all chickens were inoculated with 1 ml of a phosphate buffer saline solution containing 25 000 sporulated Eimeria acervulina oocysts/ml. The adaptive response to E. acervulina was measured by BW gain and FI from days 0 to 3 post infection (p.i.), days 3 to 5 p.i. and days 5 to 7 p.i., and by oocyst production (days 4 and 7 p.i.) and lesion scores in the duodenum (day 3, 4 and 7 p.i.). Our results demonstrated that SI temperatures in weeks 1 and 3 of incubation resulted in a reduction in yolk-free BW, chick length and navel condition. Moreover, SI temperature appeared to reduce the adaptive capacity to E. acervulina. This was demonstrated by tendencies to lower FI (P = 0.07) and BW gain (P = 0.08), more duodenal lesions (P = 0.09) and higher oocyst production (P = 0.02) after inoculation of E. acervulina. Higher lesion scores and faecal oocyst numbers were especially found when suboptimal incubation was combined with heat exposure preceding the infection. In conclusion, SI layer chickens tend to be less able to cope with an infectious challenge post hatch.